MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Rank	Gene	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 5708 to 5757 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
357	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Squared	Subtracted	0	31.36	0	31.36
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Ranked		1	94	114	20
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Measured			4977.09	5966.44	989.35
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Rooted			46.3291	53.1063	6.7772
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Squared	Divided		9811.86	7908.29	1.24071
358	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	Rooted	Subtracted	0	43.8864	44.9836	1.0972
	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]	Squared		1	34129.6	40434.5	6304.9
	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	Ranked		0	11869.9	12402.7	532.8
	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	Measured			22962	22910.9	51.1
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]		Divided		48	51	1.0625
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Ranked			16321	15577	1.04776
		Squared			0.545325	0.615621	1.12891
	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	Measured		1	5061.11	5950.22	1.17567
	nanos (fragment). [sptrembl;acc:q8wy41]	Squared	Subtracted	0	33.64	5.39669	28.2433
	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	Rooted		1	51.6736	58.4422	6.7686
	ras-related protein rab-37. [swissprot;acc:q96ax2]	Ranked			240.287	260.193	19.906
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]		Divided		243.12	266.662	1.09683
	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	Measured	Subtracted		4977.8	5966.14	988.34
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	Squared	Divided		9811.73	7908.13	1.24071
	serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955]	Rooted			61.2684	67.755	1.10587
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]			0	39.7617	37.9899	1.04664
359	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	Squared	Subtracted	1	34129.4	40434.2	6304.8
	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	Ranked	Divided		239.277	262.434	1.09678
	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	Measured	Subtracted	0	525	576	51
		Rooted			22.9129	24	1.0871
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Measured	Divided	1	12798.9	10887.2	1.17559
	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	Rooted		0	82.3645	86.1594	1.04607
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Measured			48	51	1.0625
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Ranked			16321	15577	1.04776
		Squared			0.545325	0.615621	1.12891
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]		Subtracted		98.1677	70.141	28.0267
	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]	Measured		1	1920.75	2907.43	986.68
	pescadillo homolog 1. [swissprot;acc:o00541]	Rooted	Divided		49.2488	54.4603	1.10582
	ras-related protein rab-26. [swissprot;acc:q9ulw5]	Ranked	Subtracted		240.287	260.193	19.906
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]	Squared	Divided		9812.34	7908.87	1.24068
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	Ranked	Subtracted	0	8021.78	7496.8	524.98
	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146]	Rooted		1	57.6823	64.4212	6.7389
360	60s ribosomal protein l12. [swissprot;acc:p30050]		Divided	0	27.5183	28.7547	1.04493
	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]		Subtracted		17.9172	16.833	1.0842
	alpha-nac protein. [sptrembl;acc:q9h009]	Ranked			14204.4	14724.5	520.1
	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	Rooted		1	46.901	53.624	6.723
	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]	Ranked			240.287	260.193	19.906
	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	Measured	Divided		12796.8	10886	1.17553
	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]		Subtracted	0	348.823	399.534	50.711
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Ranked	Divided		16321	15577	1.04776
		Squared			0.545325	0.615621	1.12891
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Measured			48	51	1.0625
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Squared	Subtracted		98.1677	70.141	28.0267
	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	Rooted	Divided	1	49.3771	54.5905	1.10558
	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	Ranked			243.072	266.559	1.09663

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.